Background: Stunting is one of the major causes of morbidity among under-five children Knowledge about risk factors of stunting is an important precondition for developing and strengthening nutritional intervention strategies. The purpose of this study was to assess factors associated with stunting among children of age 24 to 59 months in Meskan District of Gurage Zone, South Ethiopia. Methods: Community based case-control study was conducted among children of age 24 to 59 months. A multistage sampling technique was used to select the study participants. Cases were stunted children while controls were not stunted children. A total of 121 cases and 121 controls were studied.. Data were analyzed using SPSS 16.0 statistical software. Results: Children living in households with eight to ten [Adjusted Odds Ratio (AOR) = 4.44, 95% CI: 1.65, 11.95] and five to seven [AOR = 2.97, 95% CI: 1.41, 6.29] family members were more likely to be stunted than those living in households with two to four family members. Similarly, children living in households with three under-five children [AOR = 3.77, 95% CI: 1.33, 10.74] were more likely to develop stunting than those living in households with one under-five child. Children whose mothers worked as merchants [AOR = 4.03, 95% CI: 1.60, 10.17] were more likely to be stunted than children whose mothers worked as house wives. Children who breast fed for <2 years [AOR = 5.61, 95% CI: 1.49, 11.08] were more likely to be stunted than those who breast fed ≥2 years. Children who were exclusively breast fed for <6 months [AOR = 3.27, 95% CI: 1.21, 8.82]were more likely to develop stunting than children who were exclusively breast fed for the first 6 months. Children who bottle fed [AOR =3.30, 95% CI: 1.33, 8.17)] were more likely to be stunted than children who fed their complementary food using spoon/cup. Conclusions: Family size, number of under-five children in the household, maternal occupation, duration of exclusive breastfeeding, duration breast feeding, and method of feeding complementary food were independently associated with stunting. Thus, public health intervention working on improving child nutrition should consider these determinants.